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// File: PHyloStatistics.h
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// Created by: Julien Dutheil
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// Created on: Sat Aug 08 07:29 2009
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _PHYLOSTATISTICS_H_
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#define _PHYLOSTATISTICS_H_
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#include <Bpp/Clonable.h>
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* @brief Compute several quantities on a tree simulateously, optimizing the recursions on the tree.
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* This class uses a TreeTemplate. If the input tree is not a TreeTemplate, then a copy is performed
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* before any computation.
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* @see TreeTools, TreeTemplateTools.
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class PhyloStatistics:
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public virtual Clonable
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unsigned int numberOfLeaves_;
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unsigned int numberOfAncestors_;
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std::vector<double> branchLengths_;
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std::vector<double> nodeHeights_;
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std::vector<unsigned int> nodeDepths_;
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std::vector<unsigned int> nodeNumberOfSons_;
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std::vector<int> nodeIds_;
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numberOfLeaves_(0), numberOfAncestors_(0),
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branchLengths_(), nodeHeights_(), nodeDepths_(), nodeNumberOfSons_(), nodeIds_()
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virtual ~PhyloStatistics() {}
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#ifndef NO_VIRTUAL_COV
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clone() const { return new PhyloStatistics(*this); }
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* @brief Compute statistics for a given input tree.
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* @param tree The tree for which the statistics should be computed.
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void setTree(const Tree& tree);
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unsigned int getNumberOfLeaves() const { return numberOfLeaves_; }
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unsigned int getNumberOfAncestors() const { return numberOfAncestors_; }
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const std::vector<double>& getBranchLengths() const { return branchLengths_; }
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const std::vector<double>& getNodeHeights() const { return nodeHeights_; }
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const std::vector<unsigned int>& getNodeDepths() const { return nodeDepths_; }
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const std::vector<unsigned int>& getNodeNumberOfSons() const { return nodeNumberOfSons_; }
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const std::vector<int>& getNodeIds() const { return nodeIds_; }
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void computeForSubtree_(const Node* node, double& height, unsigned int& depth);
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} //end of namespace bpp.
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#endif //_PHYLOSTATISTICS_H_
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src/Bpp/Phyl/PhyloStatistics.h
